Summary of Study ST000688

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000487. The data can be accessed directly via it's Project DOI: 10.21228/M83S48 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000688
Study TitleBiomarkers for different types of Multiple Scelerosis (MS) (BMS vs SPMS lipidomics)
Study TypeMS analysis
Study SummaryMetabolomic Analysis in Secondary Progressive and Benign MS. Preliminary data: We have conducted whole blood cell microarray comparing gene expression profile of 20 SPMS and 13 BMS patients. The data revealed significant increase in pathways involving iron ion binding, oxygen transporter activity and hemoglobin functions. Specifically, the identified down regulated genes are involved in interacting selectively and non-covalently with iron (Fe) ions. Heme has been described as a potent pro-inflammatory molecule that can induce multiple innate immune responses, and cause excessive iron and heme-induced oxidative stress and cell death. In the brain, it causes neurodegeneration. In addition, our microarray preliminary results also show a statistically significant increase in arachidonate 12-lipoxygenase activity in SPMS compared to benign MS. Specific aim. To validate metabolites and lipid biomarkers in serum samples from patients with benign and secondary progressive MS. Our central hypothesis is that the gene expression in various types of multiple sclerosis likely create a systematic metabolomic/lipidomic environment that leads to progression in MS. We plan to compare and contrast metabolomics in SP-MS to BMS patients using the innovative technology at the Metabolomics Research Core at the University of Michigan. By monitoring lipid and metabolite changes in SP and BMS patients, we aim to identify molecular processes and biomarkers of axonal damage for MS. Then, we plan to translate such metabolomic biomarkers to correlate with our rich clinical, immunological and imaging readouts. The goal of this project is to develop a blood-based test to differentiate SP-MS from BMS patients. To accomplish this, we will first identify the gene expression signature associated with of SP-MS. Then, we will correlate these gene expression changes with lipids and metabolite changes in the blood by metabolomic network analysis. Because metabolism is the final fingerprint of functionality and has been implicated in neurodegeneration, metabolomic network analysis can be used for refining the relationships between specific gene expression and metabolites and axonal damage in progressive MS. Ultimately, we hope to develop blood, CSF and stool-based assays, and use this comprehensive profile to predict susceptibility and progression of MS. This is a new and innovative idea, which will hope to lead to future diagnostic and therapeutic development in MS.
Institute
University of Michigan
DepartmentBiomedical Research Core Facilities
LaboratoryMetabolomics core
Last NameKachman
First NameMaureen
Address6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Emailmkachman@med.umich.edu
Phone(734) 232-8175
Submit Date2017-06-05
Num Groups45
Total Subjects33
Study CommentsSee Attached document for additional information.
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2017-12-06
Release Version1
Maureen Kachman Maureen Kachman
https://dx.doi.org/10.21228/M83S48
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000487
Project DOI:doi: 10.21228/M83S48
Project Title:Biomarkers for different types of Multiple Scelerosis
Project Type:MS analysis
Project Summary:Biomarkers for Secondary Progressive and Benign Multiple Scelerosis (MS)
Institute:University of Michigan
Department:Neurology
Laboratory:Mao-Draayer Lab
Last Name:Mao-Draayer
First Name:Yang
Address:Ann Arbor, MI
Email:maodraay@umich.edu
Phone:734-615-5635

Subject:

Subject ID:SU000711
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Type of MS
SA039128S00027978Benign MS
SA039129S00027977Benign MS
SA039130S00027979Benign MS
SA039131S00027981Benign MS
SA039132S00027969Benign MS
SA039133S00027976Benign MS
SA039134S00027980Benign MS
SA039135S00027975Benign MS
SA039136S00027970Benign MS
SA039137S00027971Benign MS
SA039138S00027972Benign MS
SA039139S00027973Benign MS
SA039140S00027974Benign MS
SA039141S00027996SPMS
SA039142S00027995SPMS
SA039143S00027994SPMS
SA039144S00027997SPMS
SA039145S00028000SPMS
SA039146S00027993SPMS
SA039147S00028001SPMS
SA039148S00027999SPMS
SA039149S00027998SPMS
SA039150S00027985SPMS
SA039151S00027986SPMS
SA039152S00027984SPMS
SA039153S00027983SPMS
SA039154S00027982SPMS
SA039155S00027987SPMS
SA039156S00027988SPMS
SA039157S00027991SPMS
SA039158S00027990SPMS
SA039159S00027989SPMS
SA039160S00027992SPMS
Showing results 1 to 33 of 33

Collection:

Collection ID:CO000705
Collection Summary:-

Treatment:

Treatment ID:TR000725
Treatment Summary:-

Sample Preparation:

Sampleprep ID:SP000718
Sampleprep Summary:-
Sampleprep Protocol Filename:A004_-_Shotgun_Lipidomics.pdf

Combined analysis:

Analysis ID AN001061 AN001062
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Shimadzu CTO-20A Nexera X2 Shimadzu CTO-20A Nexera X2
Column Waters Acquity HSS T3 (50 x 2.1mm,1.8um) Waters Acquity HSS T3 (50 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type Triple TOF Triple TOF
MS instrument name ABI Sciex 5600+ TripleTOF ABI Sciex 5600+ TripleTOF
Ion Mode NEGATIVE POSITIVE
Units peak area normalized peak area normalized

Chromatography:

Chromatography ID:CH000751
Instrument Name:Shimadzu CTO-20A Nexera X2
Column Name:Waters Acquity HSS T3 (50 x 2.1mm,1.8um)
Column Temperature:55
Flow Rate:0.400uL/min
Solvent A:40% acetonitrile/60% water; 10 mM ammonium acetate
Solvent B:10% acetonitrile/5% water/85% isopropanol; 10 mM ammonium acetate
Chromatography Type:Reversed phase

MS:

MS ID:MS000956
Analysis ID:AN001061
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:Triple TOF
MS Type:ESI
Ion Mode:NEGATIVE
Analysis Protocol File:A004_-_Shotgun_Lipidomics.pdf
  
MS ID:MS000957
Analysis ID:AN001062
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:Triple TOF
MS Type:ESI
Ion Mode:POSITIVE
Analysis Protocol File:A004_-_Shotgun_Lipidomics.pdf
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